I found a way to fix this error, add bLegacyPublicIncludePaths = false; to your [ProjectName].Build.cs file (or whichever module is failing).
This requires you to fix all your header includes though, but that’s just healthy for your project.
The reason your build is failing is because legacy behavior is to append all public include paths to the build tool’s command line. This doesn’t scale and fails eventually as a project grows for tools with smaller commandline buffer. Turning off legacy include paths stops appending them to the command line at the cost of you having to put in the actual correct path for each header. But you’d want to have correct include paths anyways, right? 
UE4 has a commandlet to help with fixing your include paths:
RunUAT.bat RebasePublicIncludePaths -Project="path/to/project.uproject" -UpdateDir="path/to/code" -Write
If you have many modules you might want to turn it on for all of them, but you can also put that same boolean into your *.Target.cs files to force it for all modules in your targets.